If the hardened steel spring cup(.060 thick) that came with the heads was removed and discarded, and replaced with nothing more than a shim, I have even less confidence that your heads were set up competently.

Actually, I guess it's apparent to me at this point that they weren't.

As I mentioned previously, with an assortment of 15/30/60-thou shims, you can get within +/- .0075 of the target installed height, and you've already found they are farther off than that, and now we discover there is no longer a hardened spring locator being used.

That is not quality work.

So, IMO, it's back to my original recommendation of using the +.050 locks on all springs, only now some hardened spring locators need to be re-installed.
The "correct" locator for those springs on those heads is # 4696-16, or you can reuse the ones that came on the heads if you got them back from the machine shop with your heads.